Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
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 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGCAGTGGAACTTAGTAGCCCAGCATCCAAACTTTGATAATATCACTCAGTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaacttgccatccttatagaaaagaacaaaaataaagcaacctacctcctgatgtaatttatctgtcccatttcag

Basic information

species Zea mays
transcript GRMZM5G826714_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G826714_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 5'ss of exon 3
ACGCAGTGGAACTTAGTAGCCCAGCATCCAAACTTTGATAATATCACTCAGTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaacttgc--------catccttatagaaaagaacaaaaataaa---gcaacctacctcctgatgtaatt-tatctgtcccatt-tcag-------------------------
|| |||||||| || || || || ||||| |||||  |||||||||| ||| |||| |||||||||||||| |||||||||||||||||  |    |||||||||| || || |        |  | ||||  || | ||    | |  |   | ||       | | || |   | | ||| || | || || |                         
ACACAGTGGAATTTGGTCGCTCAACATCCTAACTTCAATAATATCACCCAGCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaatttacaaactgttctcctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttag

upper sequence: GRMZM5G826714_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G50760.1 (Glycine max), 5'ss of exon 5
---ACGCAGTGGAACTTAGTAGCCCAGCATCCAAACTTTGATAATATCACTCAGTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaacttgccatccttatagaaaagaacaaaaataaagcaacctacctcctg-atgtaatttatctgtcccatttcag----------------------------------------------------------------------------
    |  |||||||| | || |  || |||||||||||||| ||| | |||||| ||||||| |||||||||||  || | ||||| ||||||      |||||||||     |    |    | | ||       |   | ||     | ||  | |||    || ||| |   | |    |||                                                                             
TATTCTGAGTGGAACATGGTTGTTCAACATCCAAACTTTGACAATCTGACTCAGCTGTTCAGTTTCAACTACAAGTCATTGACTCCTTATGGTTCA---ATAAgtaagcgtgatcctaacttgtttcgatttctggagttaaaagctttcttaaatactgtgaatattttcttaattcttcatcataaaacatcaaaacttttacttcttattttgataaactatagaaggtaattactgatttttaagttgcttttaacag

upper sequence: GRMZM5G826714_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT3G29810.1 (Arabidopsis thaliana), 5'ss of exon 5
---ACGCAGTGGAACTTAGTAGCCCAGCATCCAAACTTTGATAATATCACTCAGTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaacttgccatccttatagaaaagaacaaaaataaagcaacctacctcctgatgtaatttatctg-tcccatttcag--
    | |||||||||||||| |  |||||||| ||||| || ||| ||||| || | ||||| |||||||||||||| |||| ||| ||   ||    |||||||||||        ||   |  |      |  |  ||  || |     |  ||  | || |||| | |  | ||  || |     
TACTCTCAGTGGAACTTAGTCGTTCAGCATCCCAACTTCGACAATCTCACTAAGCTTTTCAGTTTCAACTACAAACCGCTTAATCCTTACT-TG--AACATAAgtaagtttctcattcagattctttctcttgttcttaagaaatgtttggtttctaataatataatgttttggatcatatattgaag

upper sequence: GRMZM5G826714_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 5'ss of exon 5
---ACGCAGTGGAACTTAGTAGCCCAGCATCCAAACTTTGATAATATCACTCAGTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaacttgccatccttatagaaaagaacaaaaataaagcaacctacctcctgatgtaatttatctgtcccatttcag---------------------
   ||||||||||||||||| | |||||| || |||||||||||| | || ||| | |||||||| ||||||||  || | || || ||||  | |   ||||||||||    ||          | |  | |  |     |    | |  | | |     | ||    ||       |  |  |                     
TATACGCAGTGGAACTTAGTTGTCCAGCACCCCAACTTTGATAATCTGACCCAGATTTTCAGCTTTAACTACAAGTCATTGACACCCTATGCAGCT---ATAAgtaagt---tttaagccttcagttgtgaggctcttgttttttcctatattctttgcattttatgccatggacaaaaacttggaataatggtggcatggatcaa

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211426453|gb|FK948047.1|FK948047
EST:     CTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: CTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|18176099|gb|BM351175.1|BM351175
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTATGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|45568055|gb|CK985879.1|CK985879
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|6194735|gb|AW146839.1|AW146839
EST:     TTGTTCAGCTTCAACTACAAACCACTTACTTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: TTGTTCAGCTTCAACTACAAACCACTTAC-TCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|211426448|gb|FK948042.1|FK948042
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|24934266|gb|CA452484.1|CA452484
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|16926406|gb|BM079474.1|BM079474
EST:     CTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: CTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|71767184|gb|DR965121.1|DR965121
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|18172877|gb|BM348265.1|BM348265
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|50332123|gb|CO527249.1|CO527249
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|6194552|gb|AW146656.1|AW146656
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|211038357|gb|FL445369.1|FL445369
EST:     TGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: TGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|60340438|gb|DN207411.1|DN207411
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|83278842|gb|DV942850.1|DV942850
EST:     AAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: AAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|5847499|gb|AW000578.1|AW000578
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|50332122|gb|CO527248.1|CO527248
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|5915423|gb|AW053064.1|AW053064
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|78021136|gb|DV489523.1|DV489523
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|60355803|gb|DN222776.1|DN222776
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|37398247|gb|CF636434.1|CF636434
EST:     GGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|91871212|gb|EB401300.1|EB401300
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|60355355|gb|DN222328.1|DN222328
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|60399209|gb|DN232023.1|DN232023
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|211426451|gb|FK948045.1|FK948045
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|37379962|gb|CF626756.1|CF626756
EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|6095626|gb|AW120293.1|AW120293
EST:     GTTGTTCAGCTTCAACTACAAACCCCTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
EST: gi|211077779|gb|FL431339.1|FL431339
EST:     CACTTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTT-TGGGGGTGTAAAATTCTACAATGATCTGCTGATG
genomic: CACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCT-GGGGTGTAAAATTCTACAATGATCTGCTGATG
EST: gi|5915292|gb|AW052933.1|AW052933
EST:     TTACTCCATATGGTGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC
genomic: TTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 38

ACGCAGTGGAACTTAGTAGCCCAGCATCCAAACTTTGATAATATCACTCAGTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAGCTGCTTCTCCGCAAGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

ACGCAGTGGAACTTAGTAGCCCAGCATCCAAACTTTGATAATATCACTCAGTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAGCTGCTTCTCCGCAAGGA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 36

ACGCAGTGGAACTTAGTAGCCCAGCATCCAAACTTTGATAATATCACTCAGTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAGCTGCTTCTCCGCAAGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 164

ACGCAGTGGAACTTAGTAGCCCAGCATCCAAACTTTGATAATATCACTCAGTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaac ... cccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAGCTGCTTCTCCGCAAGGA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGCAGTGGAACTTAGTAGCCCAGCATCCAAACTTTGATAATATCACTCAGTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGTGGTGGCATAAgtaagtaaacttgccatccttatagaaaagaacaaaaataaagcaacctacctcctgatgtaatttatctgtcccatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG